Conformation of (S)-crizotinib along the reaction coordinate (Z-axis) in the MTH1 protein.

<p>Top: the PMF along the reaction coordinate. Bottom: Corresponding representatives’ structures of the (S)-crizotinib/MTH1. The proteins are shown in gray cartoon, respectively. Yellow stick representations are shown for important residues. The green stick is the ligand.</p

The secondary structure propensities of the residues in the studied peptides.

<p>The results were obtained using the time intervals of 40–200 ns.</p

Distributions of hydrophobic solvent accessible areas of WT PrP106-126 and its two mutants A117V, H111S.

<p>Hydrophobic SASA of residues Val, Met and Leu were considered.</p

The monitoring of MD trajectories.

<p>(A) Time evolution of the RMSD of all protein backbone atoms; (B) Time evolution of the RMSD of Cα atoms for the residues around 5 Å of ligand; (C) Time evolution of the RMSD of heavy atoms for the ligand; (D) Time evolution of the RMSF of Cα atoms of the protein. The values reflect the equilibration of each of the systems relative to the initial structures.</p

The side chain-side chain contact maps of WT, A117V and H111S in 40-200ns time intervals.

<p>The right column represents substracted contact maps between A117V and WT and between H111S and WT. The (i,i), (i,i±1) and (i,i±2) contacts are not included.</p

Conformation of (R)-crizotinib along the reaction coordinate (Z-axis) in the MTH1 protein.

<p>Top: the PMF along the reaction coordinate. Bottom: Corresponding representatives’ structures of the (R)-crizotinib/MTH1. The proteins are shown in gray cartoon, respectively. Yellow stick representations are shown for important residues. The blue stick is the ligand.</p

Intermolecular ligand receptor (MTH1) interaction spectrum of the MTH1-crizotinib complex according to the MM/GBSA analysis methods.

<p>Intermolecular ligand receptor (MTH1) interaction spectrum of the MTH1-crizotinib complex according to the MM/GBSA analysis methods.</p

The GUI of MolGridCal and the binding pocket of β₂AR.

<p>(A) The displayed information of GUI for monitoring MolGridCal. (B) The top three compounds, agonist, antagonist, inverse agonist bound to the pockets of β₂AR. Different ligands were represented by different colors. TOP1,2,3, agonist BI-167107, antagonist alprenolol and inverse agonist ICI 118,551 were colored in blue, red, gray, orange, yellow and green, respectively.</p

Analysis of conformation of different ligands.

<p>Delineating conformational differences between (A) TOP1-TOP3, (B) TOP1-TOP2, (C) TOP2-TOP3, (D) TOP1-BI-167107 in the pocket of β₂AR. The black oval showed the key atoms for the binding pocket of β₂AR.</p

The flowchart of virtual screening based on grid computing.

<p>MolGridCal can firstly submit the works into the server. Then the server distributed works into different nodes. The finished works would be gathered to find the candidate compounds.</p